MolNFT v1 · #75040 · protein
Crystal structure of gamma-hydroxybutyrate dehydrogenase from geobacter metallireducens in complex with NADP+
3PEF · 6-phosphogluconate dehydrogenase, NAD-binding: “Crystal structure of gamma-hydroxybutyrate dehydrogenase from geobacter metallireducens in complex with NADP+”. X-ray diffraction, 1 ligand (NAP), 16 pockets (best druggability 0.85).…
- PDB
- 3PEF
- Type
- protein
- Length
- 2,291 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, NAD-binding
- UniProt
- Q39R98
- Ligands
- NAP
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, G | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 287 | 57% helix, 14% strand | Q39R98 |
| D, E | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 286 | 57% helix, 14% strand | Q39R98 |
| F | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 285 | 56% helix, 14% strand | Q39R98 |
| H | 6-phosphogluconate dehydrogenase, NAD-binding | protein | 286 | 57% helix, 14% strand | Q39R98 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 7 copies · chains A, B, G, C, E
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, D, E, H, G
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.85 | 0.87 | 116 | GOL, NAP |
| 2 | 397 | 0.75 | 0.85 | 33 | empty |
| 3 | 469 | 0.74 | 0.83 | 60 | NAP, GOL |
| 4 | 471 | 0.74 | 0.83 | 64 | NAP, GOL |
| 5 | 476 | 0.74 | 0.82 | 66 | NAP |
Interfaces
16 interfaces between chains.
- B–D · 2335 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 2324 Ų buried · 26 hydrogen bonds · protein-protein
- F–H · 2321 Ų buried · 25 hydrogen bonds · protein-protein
- E–G · 2313 Ų buried · 24 hydrogen bonds · protein-protein
- E–H · 614 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 3PEF · Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q39R98
- Elsewhere: RCSB PDB 3PEF · PDBe 3PEF · UniProt Q39R98
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